› 2xca

X-ray diffraction
2.5Å resolution

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dGTP - MAGNESIUM FORM

Released:
DOI: 10.2210/pdb2xca/pdb
PDB entry 2xca coloured by chain, front view.
PDB entry 2xca coloured by chain, side view.
PDB entry 2xca coloured by chain, top view.
Source organisms:
Primary publication:
Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus.
Irimia A, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M
Acta Crystallogr Sect F Struct Biol Cryst Commun 66 1013-8 (2010)
PMID: 20823515

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115921 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 358 amino acids
Theoretical weight: 41.09 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*DOC)-3' Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.08 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP*TP*CP* CP*CP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.39 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DGT 1 x DGT
Ligand MG 4 x MG
2 modified residues:
Ligand DOC 1 x DOC
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P21212
Unit cell:
a: 94.443Å b: 103.909Å c: 52.707Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.259
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

DNA polymerases provide a canon of strategies for translesion synthesis past oxidatively generated lesions.
Zahn et al. (2011)
1 more

2 mentions without citation

Translesion DNA Synthesis.
Vaisman et al. (2012)
1 more